Badstuber originally tore his anterior cruciate knee ligament at the back end of 2012 against Borussia Dortmund, before rupturing the same ligament in May.
The 24-year-old travelled to Colorado for corrective surgery on Monday, with a replacement ligament inserted into his knee.
Bayern have revealed that Badstuber will return to Germany today after spending two days recovering in the USA, with work on a rehabilitation programme to begin immediately.
During the first half of last season Badstuber was a regular feature for the treble winners, forming a strong partnership in central defence alongside Dante.
Pep Guardiola's side have not put a timeline on a return to first-team action for the German international, who has played 30 times for his country.